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DNA Solvation Dynamics.

Saumyak Mukherjee1, Sayantan Mondal1, Subhajit Acharya1

  • 1Solid State and Structural Chemistry Unit , Indian Institute of Science , Bangalore 560012 , India.

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|October 3, 2018
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Summary
This summary is machine-generated.

The slow, power-law decay in DNA solvation dynamics is not caused by water but by the collective response of counterions. Molecular dynamics and Monte Carlo simulations reveal counterion hopping on the DNA backbone explains this exotic behavior.

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Area of Science:

  • Biophysics
  • Physical Chemistry
  • Computational Biology

Background:

  • DNA solvation dynamics exhibit complex multi-time scale decays, including a slow power-law component.
  • The microscopic origin of this slow decay, particularly the power-law, remains unclear.
  • Water dynamics alone do not fully explain the observed timescales.

Purpose of the Study:

  • To theoretically investigate the origins of slow power-law decay in DNA solvation dynamics.
  • To differentiate the contributions of water, counterions, and buffer ions to solvation dynamics.
  • To elucidate the microscopic mechanisms behind the exotic solvation behavior of DNA.

Main Methods:

  • Theoretical study using time-dependent statistical mechanics.
  • Application of the Oosawa model and Bagchi-Fleming-Oxtoby (BOF) continuum model.
  • Extension of the Oosawa model with continuous time random walk (CTRW) techniques.
  • Atomistic molecular dynamics (MD) simulations of a long DNA molecule.
  • Kinetic Monte Carlo (KMC) simulations of a generalized random walk model.
  • Mode coupling theory (MCT) analysis.

Main Results:

  • Water dynamics are too fast (max ~100 ps) to account for the slow power-law decay.
  • The Oosawa-BOF model fails to explain the power-law decay.
  • CTRW and KMC simulations incorporating counterion collective response and hopping on the DNA phosphate backbone successfully explain the power-law decay.
  • MD simulations confirm frequent random walks of counterions along the DNA phosphate backbone.
  • Buffer ions may contribute to logarithmic, but not power-law, time dependence.
  • Log-normal distributions of water relaxation times within DNA grooves may explain faster, multi-exponential decays at shorter timescales.

Conclusions:

  • Counterion dynamics, specifically collective response and hopping along the DNA backbone, are the primary drivers of the slow power-law decay in DNA solvation dynamics.
  • Water dynamics within DNA grooves contribute to faster, multi-exponential solvation components.
  • The study provides a comprehensive theoretical and simulation-based explanation for the complex solvation dynamics of DNA.